Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

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}

LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7280/UKB-b-7280_data.vcf.gz \
--ref-ld-chr ../reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7280/ldsc.txt \
--w-ld-chr ../reference/eur_w_ld_chr/ 

Beginning analysis at Thu Oct 17 14:40:18 2019
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/public/UKB-b-7280/UKB-b-7280_data.vcf.gz ...
Read summary statistics for 5295847 SNPs.
Dropped 1746 SNPs with duplicated rs numbers.
Reading reference panel LD Score from ../reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from ../reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1151591 SNPs remain.
After merging with regression SNP LD, 1151591 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: 0.0094 (0.0012)
Lambda GC: 1.0855
Mean Chi^2: 1.0997
Intercept: 1.01 (0.0078)
Ratio: 0.0999 (0.0784)
Analysis finished at Thu Oct 17 14:41:10 2019
Total time elapsed: 52.46s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9127,
    "inflation_factor": 1.0966,
    "mean_EFFECT": 4.0978e-06,
    "n": "-Inf",
    "n_snps": 9851866,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 45882,
    "n_est": "NA",
    "ratio_se_n": "NA",
    "mean_diff": "NaN",
    "ratio_diff": "NaN",
    "sd_y_est1": "NaN",
    "sd_y_est2": "NA",
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1151591,
    "ldsc_nsnp_merge_regression_ld": 1151591,
    "ldsc_observed_scale_h2_beta": 0.0094,
    "ldsc_observed_scale_h2_se": 0.0012,
    "ldsc_intercept_beta": 1.01,
    "ldsc_intercept_se": 0.0078,
    "ldsc_lambda_gc": 1.0855,
    "ldsc_mean_chisq": 1.0997,
    "ldsc_ratio": 0.1003
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n TRUE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio FALSE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

General metrics

  • af_correlation: Correlation coefficient between AF and AF_reference.
  • inflation_factor (lambda): Genomic inflation factor.
  • mean_EFFECT: Mean of EFFECT size.
  • n: Maximum value of reported sample size across all SNPs, \(n\).
  • n_clumped_hits: Number of clumped hits.
  • n_snps: Number of SNPs
  • n_p_sig: Number of SNPs with pvalue below 5e-8.
  • n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
  • n_ns: Number of SNPs with nonsense values:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 0 or > 1.
  • n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
  • is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
  • n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

  • n_est: Estimated sample size value, \(\widehat{n}\).
  • ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
  • mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

  • r2_sum<*>: r2 statistics under various assumptions
    • 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
    • 2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),
    • 3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),
    • 4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).

LDSC metrics

Metrics from LD regression

  • ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
  • ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
  • ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
  • ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
  • ldsc_lambda_gc: Lambda GC statistics.
  • ldsc_mean_chisq: Mean \(\chi^2\) statistics.
  • ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

  • af_correlation: abs(af_correlation) < 0.7.
  • inflation_factor: inflation_factor > 1.2.
  • n: n (max reported sample size) < 10000.
  • is_snpid_non_unique: NOT is_snpid_unique.
  • mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
  • mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
  • mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
  • mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
  • n_p_sig: n_p_sig > 1000.
  • miss_<*>: n_miss_<*> / n_snps > 0.01.
  • ldsc_ratio: ldsc_ratio > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace logical.mean logical.count numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 58 0 5294114 0 NA NA NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA NA NA
logical N 5295847 0.0000000 NA NA NA NA NA NaN : NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA NA NA 8.673275e+00 5.763598e+00 1.0000000 4.000000e+00 8.000000e+00 1.300000e+01 2.200000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA NA NA 7.852916e+07 5.657593e+07 828.0000000 3.190974e+07 6.892544e+07 1.144825e+08 2.492385e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA NA NA 4.100000e-06 3.503000e-04 -0.0026439 -2.146000e-04 2.600000e-06 2.220000e-04 2.473000e-03 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA NA NA 3.248000e-04 8.250000e-05 0.0002343 2.555000e-04 2.945000e-04 3.759000e-04 1.108100e-03 ▇▂▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA NA NA 4.859784e-01 2.926176e-01 0.0000001 2.300001e-01 4.799997e-01 7.400005e-01 1.000000e+00 ▇▇▇▆▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA NA NA 4.859787e-01 2.925924e-01 0.0000001 2.289570e-01 4.817463e-01 7.392921e-01 9.999998e-01 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA NA NA 3.394701e-01 2.437396e-01 0.0545430 1.302420e-01 2.689720e-01 5.063440e-01 9.454570e-01 ▇▃▂▂▂
numeric AF_reference 45882 0.9913362 NA NA NA NA NA NA NA 3.339149e-01 2.391199e-01 0.0000000 1.367810e-01 2.727640e-01 4.958070e-01 1.000000e+00 ▇▆▃▂▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 49298 rs200943160 T C -0.0004217 0.0004312 0.3300000 0.3281760 0.623763 0.7821490 NA
1 54676 rs2462492 C T -0.0003095 0.0004272 0.4700002 0.4688234 0.400401 NA NA
1 86028 rs114608975 T C -0.0002508 0.0006831 0.7099994 0.7135398 0.103556 0.0277556 NA
1 91536 rs6702460 G T -0.0004874 0.0004207 0.2500000 0.2466188 0.456851 0.4207270 NA
1 234313 rs8179466 C T -0.0004693 0.0008294 0.5700002 0.5714856 0.074508 NA NA
1 534192 rs6680723 C T 0.0014060 0.0004805 0.0034000 0.0034319 0.240960 NA NA
1 546697 rs12025928 A G -0.0009372 0.0005995 0.1199999 0.1179456 0.913473 NA NA
1 693731 rs12238997 A G 0.0011473 0.0004027 0.0044000 0.0043834 0.116325 0.1417730 NA
1 705882 rs72631875 G A 0.0012733 0.0005901 0.0309999 0.0309429 0.067285 0.0315495 NA
1 706368 rs55727773 A G -0.0004551 0.0002983 0.1299999 0.1271252 0.515650 0.2751600 NA
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51213613 rs34726907 C T -0.0004476 0.0003692 0.2300001 0.2253860 0.127816 0.1727240 NA
22 51216564 rs9616970 T C -0.0004571 0.0003676 0.2099999 0.2137494 0.128330 0.1563500 NA
22 51217954 rs9616974 G A -0.0006093 0.0004665 0.1900002 0.1915117 0.073314 0.0621006 NA
22 51218224 rs9616975 C A -0.0006106 0.0004667 0.1900002 0.1907743 0.073336 0.0619010 NA
22 51218377 rs2519461 G C -0.0005547 0.0004661 0.2300001 0.2340412 0.073625 0.0826677 NA
22 51219006 rs28729663 G A -0.0004423 0.0003598 0.2200002 0.2189861 0.137953 0.2052720 NA
22 51219387 rs9616832 T C -0.0006348 0.0004671 0.1700000 0.1740902 0.073747 0.0654952 NA
22 51221731 rs115055839 T C -0.0005980 0.0004674 0.2000000 0.2007096 0.073238 0.0625000 NA
22 51229805 rs9616985 T C -0.0005576 0.0004691 0.2300001 0.2345430 0.073073 0.0730831 NA
22 51237063 rs3896457 T C 0.0001891 0.0002869 0.5099998 0.5097068 0.297971 0.2050720 NA

bcf preview

1   49298   rs10399793  T   C   .   PASS    AF=0.623763 ES:SE:LP:AF:ID  -0.000421669:0.000431245:0.481486:0.623763:rs10399793
1   54676   rs2462492   C   T   .   PASS    AF=0.400401 ES:SE:LP:AF:ID  -0.000309481:0.000427227:0.327902:0.400401:rs2462492
1   86028   rs114608975 T   C   .   PASS    AF=0.103556 ES:SE:LP:AF:ID  -0.000250753:0.000683053:0.148742:0.103556:rs114608975
1   91536   rs6702460   G   T   .   PASS    AF=0.456851 ES:SE:LP:AF:ID  -0.000487383:0.000420665:0.60206:0.456851:rs6702460
1   234313  rs8179466   C   T   .   PASS    AF=0.074508 ES:SE:LP:AF:ID  -0.000469347:0.000829433:0.244125:0.074508:rs8179466
1   534192  rs6680723   C   T   .   PASS    AF=0.24096  ES:SE:LP:AF:ID  0.00140602:0.000480503:2.46852:0.24096:rs6680723
1   546697  rs12025928  A   G   .   PASS    AF=0.913473 ES:SE:LP:AF:ID  -0.000937221:0.000599455:0.920819:0.913473:rs12025928
1   693731  rs12238997  A   G   .   PASS    AF=0.116325 ES:SE:LP:AF:ID  0.00114732:0.000402686:2.35655:0.116325:rs12238997
1   705882  rs72631875  G   A   .   PASS    AF=0.067285 ES:SE:LP:AF:ID  0.0012733:0.00059009:1.50864:0.067285:rs72631875
1   706368  rs12029736  A   G   .   PASS    AF=0.51565  ES:SE:LP:AF:ID  -0.000455054:0.000298291:0.886057:0.51565:rs12029736
1   722670  rs116030099 T   C   .   PASS    AF=0.101199 ES:SE:LP:AF:ID  -0.000790753:0.00049216:0.958607:0.101199:rs116030099
1   729679  rs4951859   C   G   .   PASS    AF=0.843212 ES:SE:LP:AF:ID  -0.000613953:0.000348979:1.10237:0.843212:rs4951859
1   730087  rs148120343 T   C   .   PASS    AF=0.055911 ES:SE:LP:AF:ID  0.00174107:0.000565052:2.67778:0.055911:rs148120343
1   731718  rs58276399  T   C   .   PASS    AF=0.122307 ES:SE:LP:AF:ID  0.000979076:0.000381988:2:0.122307:rs58276399
1   734349  rs141242758 T   C   .   PASS    AF=0.121549 ES:SE:LP:AF:ID  0.000985477:0.000382148:2.00436:0.121549:rs141242758
1   736289  rs79010578  T   A   .   PASS    AF=0.13233  ES:SE:LP:AF:ID  0.000520303:0.000376645:0.769551:0.13233:rs79010578
1   752566  rs3094315   G   A   .   PASS    AF=0.838951 ES:SE:LP:AF:ID  -0.00059228:0.000337961:1.09691:0.838951:rs3094315
1   752721  rs3131972   A   G   .   PASS    AF=0.83858  ES:SE:LP:AF:ID  -0.000596083:0.000337598:1.11351:0.83858:rs3131972
1   753405  rs3115860   C   A   .   PASS    AF=0.869781 ES:SE:LP:AF:ID  -0.000976144:0.000362256:2.1549:0.869781:rs3115860
1   753541  rs2073813   G   A   .   PASS    AF=0.129871 ES:SE:LP:AF:ID  0.000955439:0.000362997:2.07058:0.129871:rs2073813
1   754182  rs3131969   A   G   .   PASS    AF=0.869123 ES:SE:LP:AF:ID  -0.00097066:0.000361546:2.13668:0.869123:rs3131969
1   754192  rs3131968   A   G   .   PASS    AF=0.869221 ES:SE:LP:AF:ID  -0.000974447:0.00036169:2.14874:0.869221:rs3131968
1   754334  rs3131967   T   C   .   PASS    AF=0.869126 ES:SE:LP:AF:ID  -0.000981196:0.000361539:2.18046:0.869126:rs3131967
1   754503  rs3115859   G   A   .   PASS    AF=0.838033 ES:SE:LP:AF:ID  -0.000577373:0.000336661:1.0655:0.838033:rs3115859
1   754964  rs3131966   C   T   .   PASS    AF=0.838664 ES:SE:LP:AF:ID  -0.000608796:0.000337607:1.14874:0.838664:rs3131966
1   755775  rs3131965   A   G   .   PASS    AF=0.839777 ES:SE:LP:AF:ID  -0.00063713:0.000342173:1.20066:0.839777:rs3131965
1   755890  rs3115858   A   T   .   PASS    AF=0.869405 ES:SE:LP:AF:ID  -0.000972355:0.000361121:2.14874:0.869405:rs3115858
1   756604  rs3131962   A   G   .   PASS    AF=0.868952 ES:SE:LP:AF:ID  -0.000965853:0.000360213:2.13668:0.868952:rs3131962
1   757640  rs3115853   G   A   .   PASS    AF=0.867905 ES:SE:LP:AF:ID  -0.000937125:0.000359522:2.04096:0.867905:rs3115853
1   757734  rs4951929   C   T   .   PASS    AF=0.869095 ES:SE:LP:AF:ID  -0.000953884:0.000360507:2.09152:0.869095:rs4951929
1   757936  rs4951862   C   A   .   PASS    AF=0.869104 ES:SE:LP:AF:ID  -0.000954273:0.000360535:2.09152:0.869104:rs4951862
1   758144  rs3131956   A   G   .   PASS    AF=0.869112 ES:SE:LP:AF:ID  -0.000954216:0.000360543:2.09152:0.869112:rs3131956
1   758626  rs3131954   C   T   .   PASS    AF=0.869589 ES:SE:LP:AF:ID  -0.000960196:0.000361533:2.10237:0.869589:rs3131954
1   760912  rs1048488   C   T   .   PASS    AF=0.838313 ES:SE:LP:AF:ID  -0.000544263:0.000336022:0.958607:0.838313:rs1048488
1   761147  rs3115850   T   C   .   PASS    AF=0.838434 ES:SE:LP:AF:ID  -0.000542341:0.000336259:0.958607:0.838434:rs3115850
1   761732  rs2286139   C   T   .   PASS    AF=0.862261 ES:SE:LP:AF:ID  -0.000873328:0.000359239:1.82391:0.862261:rs2286139
1   763394  rs3115847   G   A   .   PASS    AF=0.706753 ES:SE:LP:AF:ID  -0.000422816:0.000349717:0.638272:0.706753:rs3115847
1   766007  rs61768174  A   C   .   PASS    AF=0.105142 ES:SE:LP:AF:ID  0.0010013:0.000402871:1.88606:0.105142:rs61768174
1   768253  rs2977608   A   C   .   PASS    AF=0.761304 ES:SE:LP:AF:ID  -0.000569683:0.000285432:1.33724:0.761304:rs2977608
1   768448  rs12562034  G   A   .   PASS    AF=0.106488 ES:SE:LP:AF:ID  3.18261e-05:0.000393411:0.0268721:0.106488:rs12562034
1   769223  rs60320384  C   G   .   PASS    AF=0.129576 ES:SE:LP:AF:ID  0.000900433:0.000362781:1.88606:0.129576:rs60320384
1   771823  rs2977605   T   C   .   PASS    AF=0.868911 ES:SE:LP:AF:ID  -0.000947421:0.000360843:2.06048:0.868911:rs2977605
1   771967  rs59066358  G   A   .   PASS    AF=0.129677 ES:SE:LP:AF:ID  0.000897716:0.000362546:1.88606:0.129677:rs59066358
1   772755  rs2905039   A   C   .   PASS    AF=0.868921 ES:SE:LP:AF:ID  -0.000950928:0.00036085:2.07572:0.868921:rs2905039
1   776546  rs12124819  A   G   .   PASS    AF=0.26539  ES:SE:LP:AF:ID  0.000124806:0.000318832:0.154902:0.26539:rs12124819
1   777122  rs2980319   A   T   .   PASS    AF=0.870044 ES:SE:LP:AF:ID  -0.000928293:0.000361586:2:0.870044:rs2980319
1   777232  rs112618790 C   T   .   PASS    AF=0.095139 ES:SE:LP:AF:ID  -6.27736e-05:0.000419064:0.0555173:0.095139:rs112618790
1   778745  rs1055606   A   G   .   PASS    AF=0.128576 ES:SE:LP:AF:ID  0.000874717:0.000363014:1.79588:0.128576:rs1055606
1   779322  rs4040617   A   G   .   PASS    AF=0.128873 ES:SE:LP:AF:ID  0.000896933:0.000362398:1.88606:0.128873:rs4040617
1   780785  rs2977612   T   A   .   PASS    AF=0.868786 ES:SE:LP:AF:ID  -0.000912635:0.000360622:1.95861:0.868786:rs2977612